UNIVERSITA’ DEGLI STUDI DI NAPOLI FEDERICO II Chemical Science XXVIII Cycle Characterization and biological activity of bacterial glycoconjugates in cold adaptation. Angela Casillo Tutor: Prof. Maria Michela Corsaro Supervisor: Prof. Angela Amoresano 1 Summary Abbreviation 6 Abstract 8 Introduction Chapter I: Microorganisms at the limits of life 17 1.1 Psychrophiles 1.2 Molecular and physiological adaptation 1.3 Industrial and biotechnological applications Chapter II: Gram-negative bacteria 25 2.1 Gram-negative cell membrane: Lipopolysaccharide 2.2 Bacterial extracellular polysaccharides (CPSs and EPSs) 2.3 Biofilm 2.4 Polyhydroxyalkanoates (PHAs Chapter III: Methodology 36 3.1 Extraction and purification of LPS 3.2 Chemical analysis and reactions on LPS 3.2.1 Lipid A structure determination 3.2.2 Core region determination 3.3 Chromatography in the study of oligo/polysaccharides 3.4 Mass spectrometry of oligo/polysaccharides 3.5 Nuclear Magnetic Resonance (NMR) Results Colwellia psychrerythraea strain 34H Chapter IV: C. psychrerythraea grown at 4°C 47 4.1 Lipopolysaccharide and lipid A structures 4.1.1Isolation and purification of lipid A 4.1.2 ESI FT-ICR mass spectrometric analysis of lipid A 4.1.3 Discussion 4.2 Capsular polysaccharide (CPS) 4.2.1 Isolation and purification of CPS 4.2.2 NMR analysis of purified CPS 4.2.3 Three-dimensional structure characterization 4.2.4 Ice recrystallization inhibition assay 4.2.5 Discussion 4.3 Extracellular polysaccharide (EPS) 4.3.1 Isolation and purification of EPS 4.3.2 NMR analysis of purified EPS 4.3.3 Three-Dimensional Structure Characterization 4.3.4 Ice Recrystallization Inhibition assay 4.3.5 Discussion 4.4 Mannan polysaccharide 4.4.1 Isolation and purification of Mannan polysaccharide 4.4.2 NMR analysis 4.4.3 Ice Recrystallization Inhibition assay 4.4.4 Discussion 4.5 Polyhydroxyalkanoates (PHA) 4.5.1 Discussion Conclusion Chapter V: C. psychrerythraea grown at 8°C and -2°C 95 3 5.1 LPS purification and characterization 5.1.1 LPS purification and characterization 5.1.2 Mass Spectrometric Analysis of the O-Deacylated LOSPCP 5.2 Capsular polysaccharide CPS2 5.2.1 CPS extraction and purification 5.2.2 NMR characterization 5.2.3 Conformational analysis by NOESY 5.2.4 Ice recrystalizzation inhibition assay Conclusion Psychrobacter arcticus strain 273-4 Chapter VI: Psychrobacter arcticus strain 273-4 106 6.1 Lipopolysaccharide structure 6.1.1LPS extraction and purification 6.1.2 Deacylation of the LPS 6.1.3 Mild acid hydrolysis of the LPS 6.1.4 NMR spectroscopic analysis of OS 6.1.5 Discussion 6.2 Capsular structure 6.2.1 CPS extraction and purification 6.3 Mannan polysaccharide 6.3.1 Isolation, purification and characterization Conclusion Pseudoalteromonas haloplanktis TAC 125 Chapter VII: Pseudoalteromonas haloplanktis TAC 125: purification and characterization of an anti-biofilm molecule. 124 7.1 Isolation, purification and characterization Conclusion Experimental section Chapter VIII: Materials and methods 132 8.1 Bacteria growth 8.1.1 Colwellia psychrerythraea 34H 8.1.2 Psychrobacter arcticus 273.4 8.1.3 Pseudoalteromonas haloplanktis TAC 125 8.2 General ans analytical method 8.2.1 LPS extraction 8.2.2 CPS extraction and purification 8.2.3 EPS purification 8.2.4 Electrophoretic analysis 8.2.5 Chemical analysis 8.2.6 Mild acid hydrolysis 8.2.7 De-O and de-N-acylation of LPS 8.2.8 Ammonium hydroxide hydrolysis of lipid A 8.3 Polyhydroxyalkanoates (PHAs) extraction 8.4 Anti-biofilm molecule purification 8.5 Mass spectrometry 8.6 Nuclear magnetic resonance (NMR) 8.7 Ice recrystallization inhibition assay (IRI) 8.7.1IRI assay for CPS Colwellia psychrerythraea 4°C 8.7.2 IRI assay Bibliography 142 5 Abbreviations AFGP Antifreeze glycoproteins AFP Antifreeze proteins Ala Alanine BacN 2,4-diamino-2,4,6-trideoxy-β-glucopyranose BSCT-HMBC Band-Selective Constant Time- HMBC Cap Cold acclimation proteins Col 3,6-dideoxy-L-xylo-hexose CPS Capsular polysaccharide CSP Cold-shock proteins DEPT-HSQC Distortionless Enhancement by Polarization Transfer-Heteronuclear Single Quantum Coherence DOC-PAGE Sodium deoxycholate PolyAcrylamide Gel Electrophoresis DQF-COSY Double Quantum-Filtered Correlation spectroscopy EPS Extracellular polysaccharide ESI FT-ICR Electrospray Ionization Fourier Transform-Ion Cyclotron Resonance Et3N Triethilamine Gal Galactose GalA Galacturonic acid GalN 2-amino-2-deoxy-galactose GC-MS Gas chromatography-Mass spectrometry GIST Grid inhomogeneous sovation theory method Glc Glucose GlcA Glucuronic acid GlcN 2-amino-2-deoxy-glucose Gro Glycerol HMBC Heteronuclear multiple bond correlation HPLC High Performance Liquid Chromatography IM Inner membrane INA Ice-nucleating agents IRI Ice Recrystallization Inhibition IRMPD InfraRed MultiPhoton Dissociation Kdo 3-deoxy-D-manno-oct-2-ulosonic acid LOS Lipooligosaccharide LPS Lipopolysaccharide MALDI Matrix assisted laser desorption Man Mannose MD Molecular dynamics MGA Methyl glycoside per-acetylated MLGS Mean largest grain size NAM N-Acetylmuramic acid NMR Nuclear Magnetic Resonance NOESY Nuclear Overhauser enhancement spectroscopy OM Outer membrane PCP Phenol/Chloroform/Petroleum ethere PHA Polyhydroxyalkanoates PHB Poly(3-hydroxybutyrate) PMAA Partially Methylated Alditol Acetate Qui2NAc 2-acetamido-2,6-dideoxy-D-glucose Rha Rhamnose RMSD Root mean squared difference ROESY Rotating frame Overhauser effect spectroscopy ROS Reactive oxygen species SOD Superoxide dismutase SDS Sodium dodecyl sulphate TEM Trasmission Electronic Microscopy TFA Trifluoroacetic acid Thr Threonine TOCSY Total correlation spectroscopy TSP 3-trimethylsilyl-propanoate 7 Abstract The cryosphere, covering about one-fifth of the surface of the Earth, comprises several components: snow, river and lake ice, sea ice, ice sheets, ice shelves, glaciers and ice caps, and frozen ground which exist, both on land and beneath the oceans (Vaughan DG, et al. 2013). All these habitats, combining the low temperature and the low liquid water activity, are challenging for all the forms of life (Casanueva et al., 2010). These extreme environments are inhabited by microorganisms of all three domains of life; in particular, cold-adapted microorganisms belong to Archea and Bacteria domains. To survive in these harsh life conditions, these microorganisms have developed many adaptation strategies, including the over-expression of cold-shock and heat-shock proteins, the presence of unsaturated and branched fatty acids that maintain membrane fluidity (Chattopadhyay et al., 2006), the different phosphorylation of membrane proteins and lipopolysaccharides (Ummarino et al., 2003; Corsaro et al., 2004; Carillo et al., 2013; Casillo et al., 2015), and the production of cold-active enzymes (Huston et al., 2004), antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs), and cryoprotectants (Deming et al., 2009). Among cryoprotectants, carbohydrate-based extracellular polymeric substances (EPS) have a pivotal role in cold adaptation, as they form an organic network within the ice, modifying the structure of brine channels and contributing in the enrichment and retention of microrganisms in ice (Krembs et al., 2002; Krembs et al., 2011; Ewert et al., 2013). Macromolecules belonging to the external layer are fundamental in adaptation mechanisms, as for example the lipopolysaccharides (LPSs), which constitute the 75% of the outer membrane. LPSs have a structural role since increase the strength of bacterial cell envelope and mediate the contacts with the external environment. The general structure of an LPS is characterized by three distinct portions: the lipid A, composed of the typical glucosamine disaccharide backbone with different pattern of acylation on the two sugar residues, the core oligosaccharide, distinguishable in a inner core and a outer core, and the O-chain polysaccharide built up of oligosaccharide repeating units. This latter moiety can be absent, and in that case LPSs are named lipooligosaccharides (LOSs). n Schematic representation of a lipopolysaccharide. Since the outer membrane of Gram-negative bacteria is constituted mainly by LPSs, it is reasonable to assume that structural changes could be present in these macromolecules isolated from cold- adapted bacteria. This work has been focused especially on three different psychrophilic microorganisms, that are considered models for the study of adaptive strategies to subzero lifestyle: Colwellia psychrerythraea strain 34H Psychrobacter arcticus 273-4 Pseudoalteromonas haloplanktis TAC125 In particular, LPS molecules from C. psychrerythraea 34H grown in different conditions, and from P.arcticus, have been purified and analyzed by NMR spectroscopy and mass spectrometry. By comparing the structures obtained, especially for core oligosaccharides, it is possible to speculate that all of them are characterized by high negative charge density. This negative charge is furnished either by phosphate groups, usually linked to Kdo and lipid A saccharidic residues, or by uronic acids. These characteristics have been already found in other LPSs from psychrophilic microorganisms (Corsaro et al., 2004; Corsaro et al., 2008; Carillo et al., 2011), suggesting that such structural elements contribute to the tightness of the outer-membrane and to the association of LPS molecules through divalent cations (Ca2+ and Mg2+). GroP ↓ 3 α-L-Col-(1→2)-α-D-GalA-(1→2)-α-D-Man-(1→5)-α-Kdo4P-(2→6)-β-D-GlcN4P-(1→6)-α-D-GlcN1P LOS structure from C.psychrerythraea 34H. 9 β-D-Glc 1 ↓ 6 α-D-NAM-(1→3)-α-L-Rha-(1→3)-β-D-Gal-(1→4)-β-D-Glc-(1→4)-α-D-Glc-(1→5)-α-Kdo